6UKC

Crystal structure of a lysozyme from Litopenaeus vannamei

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298.15	HEPES 0.1M, pH 7.5, 20 (w/v) PEG 10,000%

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.368	α = 90
b = 82.368	β = 90
c = 38.665	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU	Mirrors	2009-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	41.18	86.16	0.996	8.2	2.8		6270

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.32			0.993

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LSY	2.25	35.692	6270	622	86.162	0.204	0.1998	0.2463	23.065

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.268	-0.134		-0.268		0.871

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.047
r_dihedral_angle_4_deg	22.238
r_dihedral_angle_3_deg	15.192
r_dihedral_angle_1_deg	7.681
r_lrange_it	5.68
r_lrange_other	5.654
r_scangle_it	3.16
r_scangle_other	3.158
r_mcangle_it	2.614
r_mcangle_other	2.612
r_scbond_it	1.995
r_scbond_other	1.993
r_mcbond_it	1.66
r_mcbond_other	1.659
r_angle_refined_deg	1.527
r_angle_other_deg	1.382
r_nbd_refined	0.213
r_ext_dist_refined_d	0.198
r_symmetry_nbd_other	0.195
r_nbd_other	0.186
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.11
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.068
r_symmetry_nbd_refined	0.025
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing